MTA2
protein-codingmetastasis associated 1 family member 2, the group of GATA zinc finger domain containing|NuRD complex subunits|Myb/SANT domain containing
Gene summary
This gene encodes a protein that has been identified as a component of NuRD, a nucleosome remodeling deacetylase complex identified in the nucleus of human cells. It shows a very broad expression pattern and is strongly expressed in many tissues. It may represent one member of a small gene family that encode different but related proteins involved either directly or indirectly in transcriptional regulation. Their indirect effects on transcriptional regulation may include chromatin remodeling. It is closely related to another member of this family, a protein that has been correlated with the metastatic potential of certain carcinomas. These two proteins are so closely related that they share the same types of domains. These domains include two DNA binding domains, a dimerization domain, and a domain commonly found in proteins that methylate DNA. One of the proteins known to be a target protein for this gene product is p53. Deacetylation of p53 is correlated with a loss of growth inhibition in transformed cells supporting a connection between these gene family members and metastasis. [provided by RefSeq, May 2011]
- MTA1L1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~8.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to MTA2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_004739.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 1 | 4 | |||
| missense | 54 | 54 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 6 | 6 | ||||
| Total | 0 | 0 | 63 | 1 | 0 | 64 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_004730.2 | 18 | MANE Select | |
| Ensembl | ENSP00000278823.2 | 18 | MANE Select | |
| RefSeq | NP_001317221.1 | 12 | Standard | |
| Ensembl | ENSP00000431346.1 | 12 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression
- Positive epigenetic regulation of rRNA expression
- Signal Transduction
- Epigenetic regulation of gene expression
- Gene expression (Transcription)
Biological Process
- negative regulation of transcription by RNA polymerase II
- DNA methylation
- chromatin assembly or disassembly
- regulation of fibroblast migration
- histone deacetylation
Molecular Function
- transcription regulatory region sequence-specific DNA binding
- DNA-binding transcription factor activity, RNA polymerase II-specific
- RNA polymerase II transcription factor binding
- RNA polymerase II repressing transcription factor binding
- transcription coactivator activity
Cellular Component
- histone deacetylase complex
- nuclear chromatin
- nucleus
- nucleoplasm
- transcription factor complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000278823
- Coding exons
- 18
- Length
- 8627
- Individuals with no LoFs
- 125586
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 162
- Defined
- 125748
- p
- 0.000644
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.13 | 224 | 400 | 0.560 | 0.0000235 | 4309 |
| Missense (PolyPhen) | 53 | 144 | 0.36806 | 1683 | ||
| Synonymous | -0.852 | 157 | 144 | 1.09 | 0.00000753 | 1358 |
| Loss of Function | 4.66 | 8 | 39.7 | 0.202 | 0.00000209 | 444 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0012 | 0.0011 | notable |
| Latino/Admixed American | 0.00041 | 0.00040 | rare |
| Ashkenazi Jewish | 0.00031 | 0.00030 | rare |
| East Asian | 0.0015 | 0.0014 | notable |
| Finnish | 0.00061 | 0.00060 | rare |
| European (Non-Finnish) | 0.00077 | 0.00073 | rare |
| South Asian | 0.00010 | 0.000098 | rare |
| Other | 0.00034 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May be involved in the regulation of gene expression as repressor and activator. The repression might be related to covalent modification of histone proteins.;
Recessive Scores
- pRec
- 0.278
Intolerance Scores
- LoFtool
- 0.204
- RVIS EVS
- -1.02
- RVIS percentile EVS
- 7.94
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- K
- Indispensability pred.
- E
- Indispensability score
- 0.768
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |